SMTL ID : 7ule.1

F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 27 residues within 4Å: Chain A: L.13, P.14, L.15, I.16, C.41, S.42, T.43, V.44, K.47, D.111, S.113, N.114, T.151, D.152, T.153, M.208, G.209, E.210, G.211, G.212, D.213, G.214, I.215, P.216 Chain B: L.184 Ligands: MN.3, MN.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:P.14, A:I.16, A:S.42, A:S.42, A:T.43, A:T.43, A:K.47, A:S.113, A:N.114, A:T.153, A:M.208, A:G.211, A:G.214, A:G.214, A:I.215 Water bridges: A:L.13, A:S.113, A:D.213 GDP.6: 27 residues within 4Å: Chain A: L.184 Chain B: L.13, P.14, L.15, I.16, C.41, S.42, T.43, V.44, K.47, D.111, S.113, N.114, T.151, D.152, T.153, M.208, G.209, E.210, G.211, G.212, D.213, G.214, I.215, P.216 Ligands: MN.8, MN.9 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:P.14, B:I.16, B:S.42, B:S.42, B:T.43, B:T.43, B:K.47, B:S.113, B:N.114, B:T.153, B:M.208, B:G.211, B:G.214, B:G.214, B:I.215 Water bridges: B:L.13, B:S.113, B:T.151, B:D.213

2 x F4I: (2~{S})-2-[[(2~{S})-2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[2,4,8-tris(oxidanylidene)-1,9-dihydropyrimido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxypropanoyl]amino]pentanedioic acid(Non-covalent)

F4I.2: 22 residues within 4Å: Chain A: F.94, L.96, V.106, D.111, A.112, S.113, T.153, N.154, G.155, R.156, C.157, V.162 Chain B: R.187, L.189, E.190, V.191, T.192, R.236, E.240, D.241, V.242 Ligands: NA.5 32 PLIP interactions: 15 interactions with chain B, 17 interactions with chain A Hydrophobic interactions: B:L.189, B:V.191, A:L.96, A:V.106 Hydrogen bonds: B:E.190, B:V.191, B:T.192, B:T.192, B:R.236, B:E.240, B:D.241, B:V.242, B:I.243, A:D.111, A:A.112, A:S.113, A:S.113, A:S.113, A:S.113, A:G.155 Water bridges: B:R.236, B:R.236, A:V.106, A:T.153, A:N.154, A:N.154, A:G.161, A:G.161, A:G.161 Salt bridges: B:R.187 pi-Cation interactions: B:R.236 pi-Stacking: A:F.94 F4I.7: 22 residues within 4Å: Chain A: R.187, L.189, E.190, V.191, T.192, R.236, E.240, D.241, V.242 Chain B: F.94, L.96, V.106, D.111, A.112, S.113, T.153, N.154, G.155, R.156, C.157, V.162 Ligands: NA.10 31 PLIP interactions: 17 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:L.96, B:V.106, A:L.189, A:V.191 Hydrogen bonds: B:D.111, B:A.112, B:S.113, B:S.113, B:S.113, B:S.113, B:G.155, A:E.190, A:V.191, A:T.192, A:R.236, A:E.240, A:V.242, A:I.243 Water bridges: B:V.106, B:T.153, B:N.154, B:N.154, B:G.161, B:G.161, B:G.161, A:T.192, A:R.236, A:R.236 pi-Stacking: B:F.94 Salt bridges: A:R.187 pi-Cation interactions: A:R.236

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: T.153, E.210 Ligands: GDP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.153, A:E.210, H2O.1, H2O.2 MN.4: 5 residues within 4Å: Chain A: S.42, D.111, D.152 Ligands: GDP.1, NA.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.111, A:D.152, H2O.1, H2O.2, H2O.2 MN.8: 3 residues within 4Å: Chain B: T.153, E.210 Ligands: GDP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.153, B:E.210, H2O.6, H2O.7 MN.9: 5 residues within 4Å: Chain B: S.42, D.111, D.152 Ligands: GDP.6, NA.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.111, B:D.152, H2O.6, H2O.7, H2O.8

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: D.111 Ligands: F4I.2, MN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.111 NA.10: 3 residues within 4Å: Chain B: D.111 Ligands: F4I.7, MN.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bashiri, G. et al., Poly-gamma-glutamylation of biomolecules. Nat Commun (2024)

Release Date

2023-04-12

Peptides

Coenzyme F420:L-glutamate ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Coenzyme F420:L-glutamate ligase

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